Activating Transcription
Chapter 25
25.1 Introduction
2
Figure 25.1
25.2 There Are Several Types of
Transcription Factors
• The basal apparatus
determines the startpoint for
transcription.
• Activators determine the
frequency of transcription.
3
Figure 25.2
• Activators work by making protein–protein
contacts with the basal factors.
• Activators may work via coactivators.
• Some components of the transcriptional
apparatus work by changing chromatin
structure.
4
25.3 Independent Domains Bind DNA and
Activate Transcription
• DNA-binding activity and transcription-activation are carried by
independent domains of an activator.
• The role of the DNA-binding domain is to bring the
transcription-activation domain into the vicinity of the promoter.
Figure 25.3
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25.4 The Two Hybrid Assay Detects Protein–
Protein Interactions
• The two hybrid assay works
by requiring an interaction
between two proteins:
– one has a DNA-binding
domain
– the other has a transcriptionactivation domain
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Figure 25.6
25.5 Activators Interact with the Basal
Apparatus
• The principle that governs the function of all activators
is:
– A DNA-binding domain determines specificity for the target
promoter or enhancer.
• The DNA-binding domain is responsible for localizing
a transcription-activating domain in the proximity of
the basal apparatus.
• An activator that works directly has:
– a DNA-binding domain
– an activating domain
7
• An activator that does not have an activating
domain may work by binding a coactivator that
has an activating domain.
Figure 25.7
8
• Several factors in the basal apparatus are
targets with which activators or coactivators
interact.
Figure 25.8
9
• RNA polymerase may
be associated with
various alternative sets
of transcription factors
in the form of a
holoenzyme complex.
Figure 25.9
10
25.6 Some Promoter-Binding Proteins Are
Repressors
• Repression is usually
achieved by affecting
chromatin structure.
– There are repressors
that act by binding to
specific promoters.
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Figure 25.10
25.7 Response Elements Are Recognized
by Activators
• Response elements may be located in
promoters or enhancers.
Figure 25.11
12
• Each response element is recognized by a
specific activator.
• A promoter may have many response
elements.
– Elements may in turn activate transcription
independently or in certain combinations.
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25.8 There Are Many Types of DNA-Binding
Domains
• Activators are classified according to the
type of DNA-binding domain.
• Members of the same group have
sequence variations of a specific motif that
confer specificity for individual target sites.
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25.9 A Zinc Finger Motif Is a DNA-Binding
Domain
• A zinc finger is a loop of ∼23 amino acids.
– It protrudes from a zinc-binding site formed by His and Cys amino acids.
• A zinc finger protein usually has multiple zinc fingers.
15
Figure 25.13
• The C-terminal part of
each finger forms an αhelix.
– The helix binds one turn
of the major groove of
DNA.
• Some zinc finger proteins
bind RNA instead of, or
as well as, DNA.
Figure 25.14
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25.10 Steroid Receptors Are Activators
• Steroid receptors are
examples of ligandresponsive activators.
– They are activated by
binding a steroid (or other
related molecules).
• There are separate DNAbinding and ligandbinding domains.
Figure 25.16
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25.11 Steroid Receptors Have Zinc Fingers
• The DNA binding domain of a steroid receptor is a type of zinc finger that
has Cys but not His residues.
• Glucocorticoid and estrogen receptors each have two zinc fingers.
– The first determines the DNA target sequence.
• Steroid receptors bind to DNA as dimers.
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Figure 25.17
25.12 Binding to the Response Element
Is Activated by Ligand-Binding
• Binding of ligand to
the C-terminal domain
increases the affinity
of the DNA-binding
domain for its specific
target site in DNA.
Figure 25.19
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25.13 Steroid Receptors Recognize Response
Elements by a Combinatorial Code
• A steroid response element consists of two
short half sites that may be palindromic or
directly repeated.
• There are only two types of half sites.
• A receptor recognizes its response
element by the orientation and spacing of
the half sites.
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• The sequence of the half site is recognized by
the first zinc finger.
• The second zinc finger is responsible for
dimerization, which determines the distance
between the subunits.
• Subunit separation in the receptor determines
the recognition of spacing in the response
element.
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• Some steroid receptors function as homodimers, whereas
others form heterodimers.
• Homodimers recognize palindromic response elements.
• Heterodimers recognize response elements with directly
repeated half sites.
Figure 25.20
Figure 25.21
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25.14 Homeodomains Bind Related Targets
in DNA
• The homeodomain is a DNA-binding domain of
60 amino acids that has three α-helices.
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Figure 25.24
• The C-terminal α-helix-3 is 17 amino acids and binds in the
major groove of DNA.
• The N-terminal arm of the homeodomain projects into the
minor groove of DNA.
• Proteins containing homeodomains may be either activators or
repressors of transcription.
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Figure 25.25
25.15 Helix-Loop-Helix Proteins Interact by
Combinatorial Association
• Helix-loop-helix proteins have a motif of 40 to 50 amino acids.
– The motif comprises two amphipathic α-helices of 15 to 16 residues
separated by a loop.
• The helices are responsible for dimer formation.
Figure 25.26
25
• bHLH proteins have a basic sequence adjacent
to the HLH motif that is responsible for binding
to DNA.
• Class A bHLH proteins are ubiquitously
expressed.
– Class B bHLH proteins are tissue-specific.
• A class B protein usually forms a heterodimer
with a class A protein.
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• HLH proteins that lack
the basic region prevent
a bHLH partner in a
heterodimer from
binding to DNA.
• HLH proteins form
combinatorial
associations.
– They may be changed
during development by
the addition or removal
of specific proteins.
Figure 25.27
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25.16 Leucine Zippers Are Involved in Dimer
Formation
• The leucine zipper is an amphipathic helix
that dimerizes.
• The zipper is adjacent to a basic region
that binds DNA.
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• Dimerization forms the bZIP motif:
– The two basic regions symmetrically bind inverted
repeats in DNA.
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Figure 25.28